The steady-stateorgAspecific mRNA levels inSalmonella entericaserovar Typhimurium are repressed by oxygen during logarithmic growth phase but not early-stationary phase

Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for Salmonella. Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promoters were identified using various methods such as dRNA-seq, ChIP-chip, or ChIP-Seq. However, validation using ChIP-exo, which exhibits higher-resolution performance compared to conventional ChIP, has not been conducted to date. In this study, using the representative strain S. Typhimurium LT2 (LT2), the ChIP-exo experiment was conducted to accurately determine the binding sites of catalytic RNA polymerase subunit RpoB and major sigma factors (RpoD, RpoN, RpoS, and RpoE) during exponential phase. Integrated with the results of RNA-Seq, promoters and sigmulons for the sigma factors and their association with RpoB have been discovered. Notably, the overlapping regions among binding sites of each alternative sigma factor were found. Furthermore, comparative analysis with Escherichia coli str. K-12 substr. MG1655 (MG1655) revealed conserved binding sites of RpoD and RpoN across different species. In the case of small RNAs (sRNAs), 50 sRNAs observed their expression during the exponential growth of LT2. Collectively, the integration of ChIP-exo and RNA-Seq enables genome-scale promoter mapping with high resolution and facilitates the characterization of binding events of alternative sigma factors, enabling a comprehensive understanding of the bacterial sigma factor network and condition-specific active promoters.

Strain-specific properties of Lactobacillus plantarum for prevention of Salmonella infection

Salmonella is a common food-borne pathogen; since lactobacilli show great potential for protecting against Salmonella infections, they are used as dietary supplements in functional foods. The aim of this study is to investigate the strain-specific properties and the involved mechanisms of action of Lactobacillus plantarum towards prevention of Salmonella infection. Mice were pretreated with mixed strains or single strain of Lactobacillus plantarum for 10 d prior to infection with Salmonella typhimurium SL1344, and the survival rates showed that lactobacilli exhibited strain-specific properties for preventing Salmonella infection. Then, in vitro and in vivo studies were carried out to investigate the involved mechanism of the strain-specific properties. The results showed that different Lactobacillus plantarum strains had different effects on inhibiting Salmonella growth, thus preventing adhesion to and invasion of epithelial cells by pathogens and enhancing immune responses. The present study demonstrated strain-specific properties of probiotics to prevent Salmonella infection and elucidated their underlying mechanisms.

Clinically relevant mutant DNA gyrase alters supercoiling, changes the transcriptome, and confers multidrug resistance

Bacterial DNA is maintained in a supercoiled state controlled by the action of topoisomerases. Alterations in supercoiling affect fundamental cellular processes, including transcription. Here, we show that substitution at position 87 of GyrA of Salmonella influences sensitivity to antibiotics, including nonquinolone drugs, alters global supercoiling, and results in an altered transcriptome with increased expression of stress response pathways. Decreased susceptibility to multiple antibiotics seen with a GyrA Asp87Gly mutant was not a result of increased efflux activity or reduced reactive-oxygen production. These data show that a frequently observed and clinically relevant substitution within GyrA results in altered expression of numerous genes, including those important in bacterial survival of stress, suggesting that GyrA mutants may have a selective advantage under specific conditions. Our findings help contextualize the high rate of quinolone resistance in pathogenic strains of bacteria and may partly explain why such mutant strains are evolutionarily successful.

Fluoroquinolones are a powerful group of antibiotics that target bacterial enzymes involved in helping bacteria maintain the conformation of their chromosome. Mutations in the target enzymes allow bacteria to become resistant to these antibiotics, and fluoroquinolone resistance is common. We show here that these mutations also provide protection against a broad range of other antimicrobials by triggering a defensive stress response in the cell. This work suggests that fluoroquinolone resistance mutations may be beneficial under a range of conditions.